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Sample GSM117566 Query DataSets for GSM117566
Status Public on Jun 30, 2006
Title macrophages at 24h post infection with B. melitensis strain 16M, biological rep1
Sample type RNA
 
Source name murine macrophage J774.A1 cell line, from ATCC (#TIB-67)
Organism Mus musculus
Characteristics infected with Brucella melitensis strain 16M for 24 hours
Treatment protocol J774.A1 macrophages were infected with B. melitensis strain 16M
Growth protocol J774.A1 macrophage cells were plated in 12 75-cm^2 flasks in c-DMEM without antibiotics 1 day prior to infection at a concentration of 8 x 10^6 cells per flask. Following 4h incubation at 37°C in an atmosphere containing 5% CO2, the cells were washed three times with PBS and treated with 50 ug/ml gentamicin to kill extracellular Brucella. The cells were collected for RNA isolation at 24 h post infection.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed, followed by Qiagen RNeasy Mini Kit cleanup according to the manufacturers' instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, cRNA were hybridized on GeneChip mouse 430 2.0 arrays according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Description Gene expression data from mouse J774.A1 macrophages infected with B. melitensis strain 16M for 24 hours.
Data processing The data were analyzed with GCOS using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 250.
 
Submission date Jun 30, 2006
Last update date Aug 02, 2019
Contact name Yongqun He
E-mail(s) yongqunh@umich.edu
Phone 734-615-8231
Fax 734-936-3235
URL http://www.hegroup.org/
Organization name University of Michigan
Street address 018 ARF, 1150 W. Medical Center Dr.
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL1261
Series (1)
GSE5202 Expression data from B. melitensis infected mouse macrophages
Relations
Reanalyzed by GSE119085
Reanalyzed by GSE135324

Data table header descriptions
ID_REF
VALUE GCOS-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 426.5 P
AFFX-BioB-M_at 745.1 P
AFFX-BioB-3_at 376.9 P
AFFX-BioC-5_at 1203.2 P
AFFX-BioC-3_at 1189.3 P
AFFX-BioDn-5_at 1235.6 P
AFFX-BioDn-3_at 4756.2 P
AFFX-CreX-5_at 14004.4 P
AFFX-CreX-3_at 16816.5 P
AFFX-DapX-5_at 12.5 A
AFFX-DapX-M_at 29.6 A
AFFX-DapX-3_at 4.6 A
AFFX-LysX-5_at 1.9 A
AFFX-LysX-M_at 5.5 A
AFFX-LysX-3_at 9 A
AFFX-PheX-5_at 8.9 A
AFFX-PheX-M_at 2.1 A
AFFX-PheX-3_at 26.9 A
AFFX-ThrX-5_at 32.2 A
AFFX-ThrX-M_at 4.8 A

Total number of rows: 45101

Table truncated, full table size 814 Kbytes.




Supplementary file Size Download File type/resource
GSM117566.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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